Help using Shapeit

[SeekAnswers]

I'm trying to infer haplotypes from a trio dataset using shapeit.

I have 3 VCF files for variants which I converted to plink/map PED formats with VCF tools.

I have further split the data by chromosome using pLink and I'm trying to tun shapeit on these files.

The software seemed to work well for the example dataset provided but it seems to crash for my dataset at the pruning stage without reporting any errors.

if anyone has any experience dealing with a similar project I'd like to learn about their experience.

[ffdawang]

I meet the same problem with you, have you solved it now? Can you share me your experience?

[Jeremy]

I recently used something called AlphaPhase that worked pretty fast, the downside was that it can only take bi-allelic SNPs.